Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts

Journal of Chemical Physics

Volumn 113, Issue 10, 2000, Pages 4454-4464

  Yilmaz, Lutfu Safak ^a   Atilgan, Ali Rana ^a  

^a BOGAZICI UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; CONFORMATIONS; MATHEMATICAL MODELS;

GLOBULAR PROTEINS;

PROTEINS;

EID: 0034622725     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1288512     Document Type: Article

References (35)

1. H. Frauenfelder, and B. McMahon, Proc. Natl. Acad. Sci. USA 95, 4795 (1998).
2. I. Bahar, B. Erman, R. L. Jernigan, A. R. Atilgan, and D. G. Covell, J. Mol. Biol. 285, 1023 (1999).
3. P. Zavodszky, J. Kardos, A. Svingor, and G. A. Petsko, Proc. Natl. Acad. Sci. USA 95, 7406 (1998).
4. V. A. Feher and C. Cavanagh, Nature (London) 400, 289 (1999).
5. I. Bahar, A. R. Atilgan, M. C. Demirel, and B. Erman, Phys. Rev. Lett. 80, 2733 (1998).
6. M. P. Crump, J.-H. Gong, P. Loetscher, K. Rajarathnam, A. Amara, F. Arenzana-Seisdesos, J.-L. Virelizier, M. Baggiolini, B. D. Sykes, and I. Clark-Lewis, EMBO J. 16, 6996 (1997).
7. V. Reat, H. Patzelt, M. Ferrand, C. Pfister, D. Oesterhelt, and G. Zaccai, Proc. Natl. Acad. Sci. USA 95, 4970 (1998).
8. K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan, Protein Sci. 4, 561 (1995).
9. K. A. Dill, Protein Sci. 8, 1166 (1999).
10. D. L. D. Caspar and A. Klug, CoId Spring Harbor Symp. Quant. Biol. 27, 1 (1962).
11. D. L. D. Caspar, Biophys. J. 32, 103 (1980).
12. D. E. Ingber. Annu. Rev. Physiol. 59, 575 (1997).
13. C. S. Chen, M. Mrksich, S. Huang, G. M. Whitesides, and D. E. Ingber, Science 276, 1425 (1997).
14. S. Utku, Theory of Adaptive Structures (CRC Press, New York. 1998).
15. V. J. Hilser, D. Dowdy, T. G. Oas, and E. Freire, Proc. Natl. Acad. Sci. USA 95, 9903 (1998).
16. H. Qian, and J. J. Hopfield, J. Chem. Phys. 105, 9292 (1996).
17. H. Qian, J. Chem. Phys. 109, 10015 (1998).
18. S. Miyazawa and R. L. Jernigan, Macromolecules 18, 534 (1985).
19. I. Bahar and R. L. Jernigan, J. Mol. Biol. 266, 195 (1997).
20. H. B. Callen, Thermodynamics and an Introduction to Thermostatics (Wiley, New York, 1985).
21. A. Wlodawer, H. Walter, R. Huber, and L. Sjolin, J. Mol. Biol. 180, 301 (1984).
22. A. Wlodawer, J. Deisenhofer, and R. Huber, J. Mol. Biol. 193, 145 (1987).
23. P. A. Kosen, T. E. Creighton, and E. R. Blout, Biochemistry 20, 5744 (1981).
24. T. E. Creighton and D. P. Goldenberg, J. Mol. Biol. 179, 497 (1984).
25. S. J. Hubbard, S. F. Campbell, and J. M. Thornton, J. Mol. Biol. 220. 507 (1991).
26. Z. Weng, S. Vajda, and C. Delisi, Protein Sci. 5, 614 (1996).
27. I. Bahar, A. Wallquist, D. G. Covell, and R. L. Jernigan, Biochemistry 37, 1067 (1998).
28. R. Richarz, P. Sehr, G. Wagner, and K. Wütrich, J. Mol. Biol. 130, 19 (1979).
29. G. Wagner, C. I. Stassinopolou, and K. Wütrich, Eur. J. Biochem. 145, 431 (1984).
30. D. P. Goldenberg and J. Zhang, Proteins 15, 322 (1993).
31. K. S. Kim, F. Tao, J. A. Fuchs, A. T. Danishevsky, D. Housset, A. Wlodawer, and C. K. Woodward, Protein Sci. 2, 588 (1993).
32. K. S. Kim, J. A. Fuchs, and C. K. Woodward, Biochemistry 32, 9600 (1993).
33. P. Doruker, A. R. Atilgan, and I. Bahar, Proteins 40, 512 (2000).
34. G. I. Makhatadze and P. L. Privalov, Adv. Protein Chem. 47, 307 (1995).
35. L. S. Yilmaz, M. S. thesis, Bogazici University, 2000.